New in 0.20.0 (2023-02-01)#

Major changes#

Model hyperparameter tuning is available through ModelTuner (beta) #1785,#1802,#1831.
Pre-trained models can now be uploaded to and downloaded from Hugging Face models using the hub module #1779,#1812,#1828,#1841, #1851,#1862.
AnnData .var and .varm attributes can now be registered through new fields in fields #1830,#1839.
SCBASSET, a reimplementation of the original scBasset model, is available for representation learning of scATAC-seq data (experimental) #1839,#1844 #1867,#1874,#1882.
LowLevelPyroTrainingPlan and PyroModelGuideWarmup added to allow the use of vanilla PyTorch optimization on Pyro models #1845,#1847.
Add scvi.data.cellxgene() function to download cellxgene datasets #1880.

Latent mode support changed so that user data is no longer edited in-place #1756.
Minimum supported PyTorch Lightning version is now 1.9 #1795,#1833,#1863.
Minimum supported Python version is now 3.8 #1819.
Poetry removed in favor of Hatch for builds and publishing #1823.
setup_anndata docstrings fixed, setup_mudata docstrings added #1834,#1837.
add_dna_sequence() adds DNA sequences to AnnData objects using genomepy #1839,#1842.
Update tutorial formatting with pre-commit #1850
Expose accelerators and devices arguments in Trainer #1864.
Development in GitHub Codespaces is now supported #1836.

JaxTrainingPlan now correctly updates global_step through PyTorch Lightning by using a dummy optimizer. #1791.
CUDA compatibility issue fixed in sample() #1813.
Device-backed AnnTorchDataset fixed to work with sparse data #1824.
Fix bug compute_reconstruction_error() causing the first batch to be ignored, see more details in #1854 #1857.